User:Lynmarie K Thompson/2009Chem490

Used in Spring 2009 as Sandbox 3 (so all students could edit):

'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''

L Thompson 3/1/09
 * Start by finding a protein with a known structure that interests you (see assignment sheet instructions). Determine whether anyone else in the class has already started a sandbox page for your protein (see list below). If so, join their page. If not, start a new sandbox page (you can use any unused ones listed below, or search for available numbers) and add a link to your page to our class list below (use editing button above (Ab) or follow my model).

Copy the message at the top into your sandbox page to "reserve" this sandbox for this course (others can still edit it but there is a way to go back -- not sure how yet).

Give "credit" for all your entries: add your name (like mine above) and also the source of anything that you got from another source.

Look for the pdb id for your protein in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load and display another structure.

Wow -- you can start exploring your structure now!

Task#1 (Due Wed 3/4 in the workshop). Describe the overall structure of your protein in words and make a "greenlink" illustration to go along with your description. Use the scene authoring tools and watch video 7 for instructions. Example: (L Thompson) The overall structure of green fluorescent protein is an 11-stranded beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from 1ema.

Task#2 – Find a view that shows an amphipathic element along the surface of the protein (alpha helix or beta strand or sheet -- not just a single residue). Make a green link of this view and describe it in words (ie explain colors etc). Always include your name in case others decide to join this page.

FEEDBACK: Great start -- I enjoyed your cool representations of your proteins! Please complete Task #2 if you haven't already (I fixed the wording above, which was not clear on the assignment page).

Ideas for improvements: Does your overview of the structure convey the secondary elements? (ie 5 alpha helices and 2 beta strands) I see problems with greek letters on the JMol, so best to write out alpha and beta. Be sure you include your reference to your source. Be sure you have your name on the list below.

Chem490a Sandbox pages:Student projects:
Jamal Salah & Vishwa Shah- deoxyhemoglobin (sandbox4)

Elli Schmidt - HRas p21 (sandbox5)

Abraham Khorasani - Potassium channel (streptomyces lividans) sandbox7

Marissa McGarry -  (sandbox8)

Tami Allen - Human Beta-Secretase (sandbox9)

Brendan Jones - Myosin 2 motor domain (sandbox10)

K Sniffen - ?? (sandbox11)

Bejan Hakimi & Brendan Walker- GLYCOGEN SYNTHASE KINASE 3 BETA (sandbox28)

Elaine Foun - Porin (sandbox12)

Prof Martin - T7 RNA polymerase (sandbox20)

Ankit Patel- 1bcr (sandbox314)

Minal Patel- Mitochondrial Creatine Kinase(sandbox26)

Meenal Datta - Bacteriorhodopsin(sandbox27)

David Mortenson - Fe-only hydrogenase (sandbox23)

Quoc Hung Pham - Human Serum Albumin (sandbox13)

Kevin Chen- Trypsin(sandbox21)

Tinuke Adeyemi & Niva Ran- Glucokinase (sandbox22)

Lori Mathis - acetylcholinesterase (sandbox29)

Amit Shavit & Nikola Finneran - human Beta secretase complexed with inhibitor (sandbox16)

Zachariah Blegen - Subtilisin (sandbox15)

Josef Johann Polak the Third -- Beta-2-Glycoprotein-I (Sandbox109)

Mark A. Omobono - Lipase (Sandbox313)

Jonathan Rayla- Prion Protein (Sandbox_50)

Adam Nelson - Phosphoglucose Isomerase (Sandbox 55)

Juna Jovani - Macrophage Elastase (Sandbox315)

Sophia Murray - aquaporin (Sandbox17)

Chris Baker - lac permease (Sandbox18)

Extra Credit Submissions
Mark Omobono - lysyl-tRNA synthase (ligand-less and complexed)- (Sandbox1313)

Juna Jovani - Carbonic Anhydrase (Sandbox1029)

Amit Shavit - Cytochrome P450 2C8 (Sandbox1111)

Lori Mathis- 1upg (Sandbox1988)

Niva Ran- apoB mRNA stem-loop (Sandbox1257)

Joe Polak - PlyL (work in progress) (SandboxOfTheGods)

Help Editing
Hint: Ctl-click or right-click on links below and select "Open Link in New Window"

[Help page]

[Wikimedia cheat sheet]

[General help with Wiki editing], plus more [Wiki Text examples]

Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.